| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.8.1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.8 |
| toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/0.9.29 |
| toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/0.9.21 |
| bg_diamond_view |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| diamond | 2.0.15 | package |
| Additional information about this tool |
## need to link because diamont tries to open dataset_xxx.dat.daa
ln -s '$daa' input.daa &&
diamond
view
--threads \${GALAXY_SLOTS:-1}
--daa input.daa
#if $output_section.output.outfmt == "0"
--outfmt '0'
--out '$blast_pairw'
#else if $output_section.output.outfmt == "5"
--outfmt '5'
--out '$blast_xml'
#else if $output_section.output.outfmt == "6"
--outfmt '6' #echo ' '.join(str($output_section.output.fields).split(','))
--out '$blast_tabular'
--unal $output_section.output.unal
#else if $output_section.output.outfmt == "100"
--outfmt '100'
$output_section.output.salltitles
$output_section.output.sallseqid
--out output.daa
#else if $output_section.output.outfmt == "101"
--outfmt '101'
$output_section.output.salltitles
$output_section.output.sallseqid
--out '$sam_output'
#else if $output_section.output.outfmt == "102"
--outfmt '102'
--out '$tax_output'
#end if
#if str($hit_filter.hit_filter_select) == 'max':
--max-target-seqs '$hit_filter.max_target_seqs'
#else:
--top '$hit_filter.top'
#end if
$forwardonly
--compress '0'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
daa: diamond_results.daa output_section|output|outfmt: 5 hit_filter|max_target_seqs: 1 hit_filter|hit_filter_select: max |
name: value |
diamond_results.daa value |
| Test-2 |
daa: diamond_results.daa output_section|output|fields: ['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore', 'cigar', 'scovhsp'] output_section|output|outfmt: 6 |
name: value |
diamond_results.daa value |
| Test-3 |
daa: diamond_results.daa output_section|output|outfmt: 101 hit_filter|hit_filter_select: top forwardonly: True |
name: value |
diamond_results.daa value |